A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/lustre1/home/mass/amalia/montipora_mapping/outputs/stringtie
General Statistics
| Sample Name | Assigned | Assigned |
|---|---|---|
| SRR14864064 | 28.0M | 28.1% |
| SRR14864065 | 22.5M | 25.0% |
| SRR14864066 | 17.4M | 19.2% |
| SRR14864067 | 38.7M | 50.2% |
| SRR14864068 | 32.4M | 49.6% |
| SRR14864069 | 37.8M | 55.3% |
| SRR14864070 | 38.5M | 55.9% |
| SRR14864071 | 39.9M | 48.6% |
| SRR14864072 | 34.1M | 49.8% |
GffCompare
0.12.9
Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.URL: https://ccb.jhu.edu/software/stringtie/gffcompare.shtmlDOI: 10.12688/f1000research.23297.1
Accuracy values
Displayed are the accuracy values precisiond and sensitivity for different levels of genomic features. The metrics are calculated for the comparison of a query and reference GTF file.
Accuracy metrics are calculated as described in Burset et al. (1996). Sensitivity is the true positive rate, Precision True Positives are query features that agree with features in the reference. The exact definition depends on the feature level:
- Base: True positives are bases reported at the same coordinates.
- Exon: Comparison units are exons that overlap in query and reference with same coordinates.
- Intron chain: True positives are query transcripts for which all introns coordinates match those in the reference.
- Transcript: More stringent then intron chain, all Exon coordinates need to match. Outer exon coordinates (start + end) can vary by 100 bases in default settings
- Locus: Cluster of exons need to match.
A more in depth description can be found here.
Novel features
Number of novel features, present in the query data but not found in the reference annotation.
Missing features
False negative features, which are found in the reference annotation but missed (not present) in the query data.
featureCounts
Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.URL: http://subread.sourceforge.netDOI: 10.1093/bioinformatics/btt656
Assignments
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| GffCompare | 0.12.9 |